Kohli, the only India batsman to pass 50, made 116 from 120 balls because his side were bowled out to 250 in 48.2 overs.
At the 45th over, the vacationers were nicely placed at 218-6 in reply but lost their last five wickets for 24 runs.
11 was had by them from the final.
A partnership of 83 between Usman Khawaja and openers Aaron Finch gave Australia’s pursuit a great start and, despite the loss of routine wickets , they looked by a sixth-wicket stand of 47 between Alex and Stoinis Carey at control.
But with 38 runs needed from the last 3 6 balls, Carey was bowled by Kuldeep Yadav for 22 after which Jasprit Bumrah, that finished from his 10 overs with amounts of 2-29, disregarded Nathan Coulter-Nile and Pat Cummins.
All rounder Shankar was made to bowl the 50th over and he drifted Stoinis lbw along with his shipping and then sealed the win by bowling person Adam Zampa.
Shankar (46) had earlier put on 81 together with Kohli, who dragged his team into a defendable total.
Despite having appeared at over half the number of games played with India legend Sachin Tendulkar, the 31, kohli is now nine centuries in short supply of the ODI album.
India lead the string 2-0.